To begin this lesson, type source $ZAP_DEMO to the unix cshell prompt. This script makes a new directory in your account titled "zap1.0S_demo" which has soft links to the master Zap tutorial directory. Type cd zap1.0S_demo to change to this new tutorial directory. Then enter the command sybyl to load and run SYBYL.

From the menubar go to the File pulldown and select the Read... command. A list of available files in the current directory appears in the dialog box. If you select Molecule from the File Type menu, the directory list will be filtered (by filename extension) to include only files that are likely to be molecular data. The file "DHFR_MTX.mol2" is an adaptation of "1rg7.pdb" where water molecules have been deleted, errors in Sybyl atom and bond type assignment (carboxylate oxygens not assigned as O.co2, the N1 atom not protonated, and incorrect bonding around the amine), hydrogens have been added to both the dihydrofolate reductase (DHFR) enzyme and the methotrexate inhibitor (MTX), the hydrogens of the resulting complex were optimized, and the enzyme and inhibitor have been separated into two molecular areas. Select DHFR_MTX.mol2 (recommended) if you wish to bypass the "educational" experience of correcting Sybyl's problems with the PDB. Press the OK button. The dihydrofolate reductase enzyme should be displayed in the SYBYL M1 molecular display area and methotrexate should be displayed in the SYBYL M2 area.

You can alternately display either of these molecules by turning D1 or D2 on/off with the Checkbox icon. The charges attached to these molecules were calculated with the Sybyl Gasteiger-Hückel algorithm. The atomic potential calculated by Zap uses atomic charge as input, so the cahrge model used may make a difference.

Now, pulldown eslc to Zap; select Atom Potentials & Energies.... This invokes the Zap Molecule Potentials dialog box after a brief warning of the consequences. (The current atomic charges will be replaced by the potentials.) First we must select the Atoms.... In the Atom Expression dialog box verify that M2 is the chosen molecular area and press the All push button to select all atoms of methotrexate. (Press OK.) We will Display the Atom Potential and will use Calc. Resolution of Medium. Use the suggested Dielectric Constants of 2.00 for Inside and 80.00 for Outside. Press the More Zap Details... button to active the Zap Details dialog and select kcal/mol for the display Units. Dielectric Model should be Gaussian. The default Convergence parameters are fine. Likewise leave the default Zap VDW radius for H and Zap Salt Concentration, although it may be fun to explore these options later. Press OK in the Details dialog and OK in the Potentials dialog. The calculation is actually quite a bit faster than the ability of Sybyl (through SPL) to display the potentials.

Potentials for MTX in solvent

When Sybyl has finished updating the Atom Potentials, we will set the display for M4 to be only MTX. Select the Undisplay Atoms command from View and select MTX from M4 (using the Substructures... button). Press Invert to Undisplay the rest of M4, i.e., the enzyme. Now, with the Checkbox icon, make sure that M1 and M3 are turned off, and flip back and forth between M2 (where the potentials for MTX were calculated as in solution) and M4 (where the potentials of MTX were calculated in the site.

Potentials for MTX in "site"